Nitrate-dependent anaerobic ferrous oxidation (NAFO) is a newly discovered biological denitrification process that can effectively remove nitrate from wastewater lacking organic carbon source and has a good development prospect in practical engineering applications. In order to reduce the start-up cost of the reaction and improve the treatment efficiency, the special sludge for anaerobic tank and anaerobic granular sludge were selected to compare and evaluate the operation effect of the NAFO process. Two CSTR reactors with the same reaction conditions were constructed and were operated continuously for 56 days. Then, on the basis of comparative operation experiments, the influencing factors of the nitrate treatment effect were studied. The anaerobic granular sludge with superior performance was used for single factor experiments to investigate the effects of the initial inorganic carbon source to nitrate ratio (IC/N), the initial ferrous to nitrate ratio (Fe/N) and the initial pH on nitrate removal performance. The results showed that the nitrate treatment efficiency of the two reactors reached more than 80% after 14 days of operation, and the reactor with anaerobic granular sludge showed higher performance, with the average and maximum nitrate removal efficiency of 79.4% and 92.9%, respectively, and the average nitrate removal rate of 0.045 kg-N/(m^3·d); When anaerobic granular sludge was used as seed sludge for reaction, the NAFO process had the best effect on nitrate treatment under the conditions of IC/N of 12.68, Fe/N of 3.82, and pH of 6.46 for the initial influent.